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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:42, 17 September 2013


Full id: C145_neuroblastoma_peripheral_neuroectodermal_neuroepithelioma_carcinoid_adult_extraskeletal



Phase1 CAGE Peaks

Hg19::chr10:115469134..115469144,+p11@CASP7
Hg19::chr10:130493765..130493772,+p@chr10:130493765..130493772
+
Hg19::chr10:19206477..19206486,-p@chr10:19206477..19206486
-
Hg19::chr11:111061427..111061435,-p@chr11:111061427..111061435
-
Hg19::chr11:126898086..126898090,-p@chr11:126898086..126898090
-
Hg19::chr12:20097309..20097312,+p@chr12:20097309..20097312
+
Hg19::chr13:19866903..19866909,-p@chr13:19866903..19866909
-
Hg19::chr13:19866912..19866922,-p@chr13:19866912..19866922
-
Hg19::chr13:19867186..19867230,-p@chr13:19867186..19867230
-
Hg19::chr13:21817233..21817255,+p@chr13:21817233..21817255
+
Hg19::chr13:31573586..31573598,-p@chr13:31573586..31573598
-
Hg19::chr13:31576161..31576165,-p@chr13:31576161..31576165
-
Hg19::chr13:31586634..31586639,-p@chr13:31586634..31586639
-
Hg19::chr13:31590717..31590730,-p@chr13:31590717..31590730
-
Hg19::chr13:98503553..98503558,-p@chr13:98503553..98503558
-
Hg19::chr14:96944793..96944803,+p@chr14:96944793..96944803
+
Hg19::chr15:101818299..101818304,-p@chr15:101818299..101818304
-
Hg19::chr15:70867778..70867780,-p@chr15:70867778..70867780
-
Hg19::chr16:57880370..57880384,-p8@KIFC3
Hg19::chr16:8626896..8626903,+p@chr16:8626896..8626903
+
Hg19::chr16:8626925..8626935,+p@chr16:8626925..8626935
+
Hg19::chr16:8626942..8626951,+p@chr16:8626942..8626951
+
Hg19::chr16:8626961..8626972,+p@chr16:8626961..8626972
+
Hg19::chr16:8627043..8627056,+p@chr16:8627043..8627056
+
Hg19::chr16:8627138..8627146,+p@chr16:8627138..8627146
+
Hg19::chr18:3742467..3742480,-p19@DLGAP1
Hg19::chr18:56886837..56886844,+p@chr18:56886837..56886844
+
Hg19::chr18:56886851..56886854,+p@chr18:56886851..56886854
+
Hg19::chr18:56892776..56892782,+p6@GRP
Hg19::chr18:77044132..77044175,+p@chr18:77044132..77044175
+
Hg19::chr1:12710326..12710358,+p@chr1:12710326..12710358
+
Hg19::chr1:177701516..177701535,-p@chr1:177701516..177701535
-
Hg19::chr1:201328857..201328867,-p@chr1:201328857..201328867
-
Hg19::chr1:209796957..209796972,-p4@MIR4260
Hg19::chr1:209796983..209796993,-p6@MIR4260
Hg19::chr1:209797028..209797042,-p3@MIR4260
Hg19::chr1:209797044..209797052,-p7@MIR4260
Hg19::chr1:209797057..209797070,-p5@MIR4260
Hg19::chr1:209798010..209798013,-p@chr1:209798010..209798013
-
Hg19::chr1:209798058..209798063,-p@chr1:209798058..209798063
-
Hg19::chr1:236451669..236451673,+p@chr1:236451669..236451673
+
Hg19::chr1:236818586..236818597,+p@chr1:236818586..236818597
+
Hg19::chr1:247615972..247615977,-p@chr1:247615972..247615977
-
Hg19::chr1:39045718..39045723,-p@chr1:39045718..39045723
-
Hg19::chr1:60324644..60324660,+p@chr1:60324644..60324660
+
Hg19::chr1:72475310..72475318,+p@chr1:72475310..72475318
+
Hg19::chr20:24607850..24607857,-p@chr20:24607850..24607857
-
Hg19::chr20:24608066..24608086,-p@chr20:24608066..24608086
-
Hg19::chr20:24608551..24608564,-p@chr20:24608551..24608564
-
Hg19::chr20:24608570..24608595,-p@chr20:24608570..24608595
-
Hg19::chr20:24608639..24608641,-p@chr20:24608639..24608641
-
Hg19::chr20:49393105..49393130,+p@chr20:49393105..49393130
+
Hg19::chr21:27922896..27922913,+p@chr21:27922896..27922913
+
Hg19::chr21:27924233..27924255,+p@chr21:27924233..27924255
+
Hg19::chr21:27924313..27924341,+p@chr21:27924313..27924341
+
Hg19::chr21:27941000..27941004,+p@chr21:27941000..27941004
+
Hg19::chr21:28022135..28022171,+p@chr21:28022135..28022171
+
Hg19::chr21:28025780..28025786,+p@chr21:28025780..28025786
+
Hg19::chr21:28083005..28083006,+p@chr21:28083005..28083006
+
Hg19::chr21:46341022..46341041,+p2@ENST00000441379
p2@uc002zgh.2
Hg19::chr2:121797299..121797304,+p@chr2:121797299..121797304
+
Hg19::chr2:152185906..152185915,-p@chr2:152185906..152185915
-
Hg19::chr2:152185920..152185940,-p@chr2:152185920..152185940
-
Hg19::chr2:152185966..152185977,-p@chr2:152185966..152185977
-
Hg19::chr2:152186077..152186088,-p@chr2:152186077..152186088
-
Hg19::chr2:152186116..152186128,-p@chr2:152186116..152186128
-
Hg19::chr2:152186130..152186137,-p@chr2:152186130..152186137
-
Hg19::chr2:178013069..178013115,-p@chr2:178013069..178013115
-
Hg19::chr2:208528667..208528672,+p@chr2:208528667..208528672
+
Hg19::chr2:234265736..234265757,+p@chr2:234265736..234265757
+
Hg19::chr2:234265804..234265830,+p@chr2:234265804..234265830
+
Hg19::chr2:234699417..234699436,+p@chr2:234699417..234699436
+
Hg19::chr2:234699439..234699454,+p@chr2:234699439..234699454
+
Hg19::chr2:234699458..234699476,+p@chr2:234699458..234699476
+
Hg19::chr2:234699501..234699508,+p@chr2:234699501..234699508
+
Hg19::chr2:234699525..234699537,+p@chr2:234699525..234699537
+
Hg19::chr2:234699597..234699619,+p@chr2:234699597..234699619
+
Hg19::chr3:126191239..126191272,-p11@ZXDC
Hg19::chr3:197808599..197808629,-p@chr3:197808599..197808629
-
Hg19::chr3:197836976..197836989,+p1@ENST00000419104
p1@ENST00000422555
Hg19::chr3:58223326..58223335,+p5@ABHD6
Hg19::chr4:159766833..159766839,-p@chr4:159766833..159766839
-
Hg19::chr4:166503334..166503340,+p@chr4:166503334..166503340
+
Hg19::chr4:41750793..41750804,-p5@PHOX2B
Hg19::chr4:72897707..72897731,+p1@NPFFR2
Hg19::chr4:72897735..72897749,+p3@NPFFR2
Hg19::chr4:72897772..72897779,+p6@NPFFR2
Hg19::chr4:72897784..72897795,+p2@NPFFR2
Hg19::chr4:72897809..72897820,+p4@NPFFR2
Hg19::chr5:124007135..124007142,+p@chr5:124007135..124007142
+
Hg19::chr5:42970980..42970988,+p@chr5:42970980..42970988
+
Hg19::chr5:43033953..43033958,+p@chr5:43033953..43033958
+
Hg19::chr6:123160336..123160346,+p@chr6:123160336..123160346
+
Hg19::chr6:123160905..123160921,+p@chr6:123160905..123160921
+
Hg19::chr6:123160933..123160937,+p@chr6:123160933..123160937
+
Hg19::chr6:123194886..123194889,+p@chr6:123194886..123194889
+
Hg19::chr6:14537245..14537253,-p@chr6:14537245..14537253
-
Hg19::chr6:16804682..16804686,+p@chr6:16804682..16804686
+
Hg19::chr6:3939499..3939502,-p@chr6:3939499..3939502
-
Hg19::chr6:83931577..83931579,+p@chr6:83931577..83931579
+
Hg19::chr7:31232388..31232398,-p@chr7:31232388..31232398
-
Hg19::chr7:41976787..41976795,+p@chr7:41976787..41976795
+
Hg19::chr7:7553032..7553040,+p@chr7:7553032..7553040
+
Hg19::chr8:2072348..2072354,-p@chr8:2072348..2072354
-
Hg19::chr8:26723933..26723943,-p@chr8:26723933..26723943
-
Hg19::chr8:27041862..27041872,+p1@ENST00000521408
Hg19::chr8:28174496..28174516,+p3@PNOC
Hg19::chr8:28200458..28200480,+p@chr8:28200458..28200480
+
Hg19::chr8:37560262..37560269,-p@chr8:37560262..37560269
-
Hg19::chr8:70745541..70745555,-p3@SLCO5A1
Hg19::chr8:97136855..97136857,-p@chr8:97136855..97136857
-
Hg19::chr8:97173993..97174018,-p@chr8:97173993..97174018
-
Hg19::chr8:97174234..97174264,-p@chr8:97174234..97174264
-
Hg19::chr8:97178060..97178066,+p@chr8:97178060..97178066
+
Hg19::chr9:90112117..90112164,+p19@DAPK1
Hg19::chrX:135918268..135918276,+p@chrX:135918268..135918276
+
Hg19::chrX:25034686..25034690,-p@chrX:25034686..25034690
-
Hg19::chrX:2712069..2712080,+p6@XG


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0005184neuropeptide hormone activity0.0115249039428662



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
sympathetic nervous system4.21e-215
autonomic nervous system4.21e-215
peripheral nervous system2.19e-128
Disease
Ontology termp-valuen
neuroectodermal tumor2.00e-4010
germ cell and embryonal cancer3.41e-1922
germ cell cancer3.41e-1922
neuroendocrine tumor7.67e-186


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10
MA0004.10.0565112
MA0006.10.000978155
MA0007.10.0450115
MA0009.10.248015
MA0014.19.7901e-06
MA0017.10.0513533
MA0019.10.0341099
MA0024.10.630888
MA0025.10.799003
MA0027.11.37206
MA0028.10.0690455
MA0029.12.53772
MA0030.10.650119
MA0031.10.110404
MA0038.10.283071
MA0040.10.390885
MA0041.11.06421
MA0042.11.13751
MA0043.10.248338
MA0046.12.40572
MA0048.16.07116e-06
MA0050.10.104556
MA0051.10.274812
MA0052.10.176353
MA0055.10.0439011
MA0056.10
MA0057.16.02951
MA0058.10.00438593
MA0059.10.00427338
MA0060.17.29403e-05
MA0061.10.0120204
MA0063.10
MA0066.10.0677511
MA0067.10.232687
MA0068.10.0203374
MA0069.10.503043
MA0070.11.76124
MA0071.10.35669
MA0072.11.24668
MA0073.13.29221e-13
MA0074.10.00341137
MA0076.10.0186902
MA0077.11.70443
MA0078.10.144239
MA0081.11.06219
MA0083.10.0734466
MA0084.10.956227
MA0087.10.47048
MA0088.13.26741
MA0089.10
MA0090.10.613112
MA0091.13.97497
MA0092.10.152865
MA0093.10.0275482
MA0095.10
MA0098.10
MA0100.10.500459
MA0101.10.0293056
MA0103.10.745313
MA0105.11.63501e-05
MA0106.11.15596
MA0107.10.0128364
MA0108.20.790411
MA0109.10
MA0111.10.0288359
MA0113.10.232155
MA0114.10.00160026
MA0115.10.18566
MA0116.10.00589818
MA0117.10.287891
MA0119.10.0269128
MA0122.10.0955865
MA0124.10.487829
MA0125.10.760711
MA0130.10
MA0131.10.0127266
MA0132.10
MA0133.10
MA0135.10.280005
MA0136.11.65621
MA0139.10.000542715
MA0140.11.33018
MA0141.10.0340398
MA0142.11.42391
MA0143.10.916479
MA0144.12.41923
MA0145.10.000893049
MA0146.11.21553e-13
MA0147.10.0314773
MA0148.10.417974
MA0149.1352.096
MA0062.20.000241871
MA0035.21.66348
MA0039.22.39703e-10
MA0138.20.145457
MA0002.20.0196477
MA0137.20.442545
MA0104.20.00270289
MA0047.20.546254
MA0112.20.000246785
MA0065.20.0039906
MA0150.10.178743
MA0151.10
MA0152.10.790063
MA0153.10.725224
MA0154.10.000284881
MA0155.10.00032307
MA0156.10.136909
MA0157.10.0747125
MA0158.10
MA0159.10.565255
MA0160.10.17399
MA0161.10
MA0162.11.71356e-12
MA0163.11.69454e-11
MA0164.10.678038
MA0080.21.03811
MA0018.20.0976923
MA0099.20.0479845
MA0079.20.507112
MA0102.20.393325
MA0258.10.123345
MA0259.10.000200094
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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